You should still be able to go to www.hotmail.com and login there to view what's hanging out on the server. The mail icon on the ipad functions just like a mail application on a computer, pulling messages down from the server. It only downloads so many message so after a while this might fix itself if it's a bad message, or you can login at hotmail.com using safari and remove messages, or move them to a folder and see if that does the trick. It's just a guess. I just found that's what was going on with my issue. I've worked at ISP's in the past and it comes up now and again.
You might need to remove and re-add your mail settings from the settings icon, then mail. I would do this before removeing messages from the server, and then following removeing messages. Select the account then, delete account. Create it from scratch, just in case the account settings have gotten corupted or are not set correctly. This will also force the iPad to pull information off the server.